Prior to playing for Tottenham Hotspur and Borussia Dortmund, Lee started his professional career at FC Seoul, then known as Anyang LG Cheetahs in the Korean K League 1 and then spent two years with PSV Eindhoven of the Netherlands, earning high acclaim from PSV Coach Guus Hiddink, who had previously coached Lee and South Korea during the 2002 World Cup. Recognized as the best left-back in the Netherlands after the 2004–05 season, Tottenham signed him amidst heavy competition with several Serie A clubs. He transferred to Tottenham in August 2005.

On 19 November 2008, Lee became the seventh Korean player to earn 100 caps in a World Cup qualifier against Saudi Arabia. During the 2011 AFC Asian Cup, Lee captained the national team twice after the substitutions of the regular Korean captain, Park Ji-sung.

At PSV, Lee flourished under Hiddink's guidance and soon established himself in PSV's first team. Known for his endurance, technique, and ability in both defence and attack, Lee was widely regarded as the best left-back in the Dutch Eredivisie. Lee and his compatriot Park were instrumental in PSV Eindhoven's run to the 2005 UEFA Champions League semi-final, although to their disappointment, they were knocked out by AC Milan.

Despite PSV's persistent attempts to keep him, Lee moved to the English club Tottenham Hotspur in August 2005.

At Tottenham, Lee was an immediate hit and earned a spot on the Premier League's best eleven in his debut week. Tottenham coach Martin Jol, at the time of his signing on 31 August 2005, touted him as "the best left-back in Holland."[2][3] His form did however fluctuate in the 2005–06 season despite them being almost ever present in a defence which conceded the fourth lowest number of goals in that season.

In the beginning of 2006–07 season, Lee moved to right full-back due to Benoît Assou-Ekotto's impressive pre-season performance and an injury to regular right-back Stalteri. Lee then faced increased competition when Tottenham signed French defender Pascal Chimbonda on the final day of the transfer period. Lee also suffered a knee injury and in August 2006, Tottenham offered his rights to A.S. Roma of Italy's Serie A, but he backed out at the last minute for "personal reasons". An Italian media report said religion played a part in his decision to reject the transfer offer. On 31 August 2006, Lee held a press conference in Korea and denied that religion was a factor in his decision. He said that moving to Roma would have been great for him in terms of football alone but he decided against it for personal reasons that he would not reveal, despite being pressed for answers by 50 attending reporters.[5]

Lee regained his place in the first team when Assou-Ekotto's form began to falter, most notably in a very poor performance against arch-rivals Arsenal. Lee came on as a half-time substitute in that match and was a notable improvement, and was again preferred by Jol for the starting eleven, until a season-ending knee injury sustained in a UEFA Cup Quarterfinal match against Sevilla on 5 April.[6]

On 9 August 2007, Tottenham manager Martin Jol announced that Lee would be "fit for selection" in "one or two weeks".[7] On 18 August 2007, Lee made his first start of the season against Derby County.

Lee officially signed with Vancouver on 6 December 2011.[11] He scored his first MLS goal for Vancouver on 28 April 2012 off a free kick against the Columbus Crew. Lee was a crucial part to Vancouver's 2012 season and was played as a right back. He was considered one of their best players on the team that year. Lee was awarded with Vancouver's 2012 Player of the Year on 21 October 2012[12] after helping the team become the first Canadian team to reach the MLS Cup Playoffs.

He played his final professional game on 27 October 2013 in Vancouver in 3–0 win against the Colorado Rapids. After scoring the first and eventual game-winning goal, 2013 MLS Golden Boot-winner Camilo Sanvezzo presented Lee with the ball during the goal celebration.[13]